There are many reasons for separating urine from human feces. One of them is to use this waste product as a liquid fertilizer. Urine is more than 65% water and of the impurities present, nitrogen and phosphorus are the most abundant composing 18-23% of the urine. By collecting the urine in containers and diluting it by adding water, farmers can directly apply this solution to their crops and reduce their dependence on expensive chemical fertilizers. Another reason is to keep the moisture and nitrogen content in the composting toilet ideal. There is far more nitrogen present in urine than feces, which can really upset the C/N ratio (explained in composting factors page) requiring far more carbon material to be added to the compost toilet than if the urine was collected separately. The addition of urine can also saturate the compost pile well beyond the desirable moisture content causing anaerobic conditions to prevail, composting to be replaced by fermentation and foul odors to persist.
There is also an argument for not diverting the urine because there is valuable nitrogen and moisture necessary for good composting. Adding the urine would require adding far more carbon material to the pile as explained above but the argument is that urine and human feces cannot be composed alone. The diluted urine that is applied to crops should be composted first because the form of nitrogen present usually requires composting to be made available to crops, otherwise it simply volatilizes into the atmosphere. By composting feces and urine together, you can be guaranteed to get a compost high in plant available nitrogen and other organic materials. Composting feces alone will likely result in a nitrogen poor compost unless another nitrogen source is added like grass clippings or other vegetative matter.